library(dplyr)
library(magrittr)
load(params$RData_image)

The haplotype of each sample is stored in the table aacigar_table within the object drug_resistant_haplotypes_plot.

library(tmap)
tmap_mode('view')
drug_resistant_haplotypes_plot$i_drug_map
drug_resistant_haplotypes_plot$drug_phenotyope_lineplot
**Figure 2:** Frequency of haplotypes carrying mutations associated with resistance to Chloroquine, Lumefantrine...(panels). y-axis shows the frequency in each population, x-axis shows the quarter of the year where the sample was collected, rows panels corresponds to the study areas, and column panels represents each Drug. Colors were assigned based on the possible phenotype, blue indicates sensitive, red indicates resistance, and gloden represent haplotypes carrying mutations respect to the reference strain but that haven't been associated with resistance.

Figure 2: Frequency of haplotypes carrying mutations associated with resistance to Chloroquine, Lumefantrine…(panels). y-axis shows the frequency in each population, x-axis shows the quarter of the year where the sample was collected, rows panels corresponds to the study areas, and column panels represents each Drug. Colors were assigned based on the possible phenotype, blue indicates sensitive, red indicates resistance, and gloden represent haplotypes carrying mutations respect to the reference strain but that haven’t been associated with resistance. 

drug_resistant_haplotypes_plot$drug_phenotype_barplot
**Figure 3:** Frequency of haplotypes carrying mutations associated with resistance to Chloroquine, Lumefantrine...(panels). y-axis shows the frequency in each population, x-axis shows the quarter of the year where the sample was collected, rows panels corresponds to the study areas, and column panels represents each Drug. Colors were assigned based on the possible phenotype, blue indicates sensitive, red indicates resistance, and gloden represent haplotypes carrying mutations respect to the reference strain but that haven't been associated with resistance.

Figure 3: Frequency of haplotypes carrying mutations associated with resistance to Chloroquine, Lumefantrine…(panels). y-axis shows the frequency in each population, x-axis shows the quarter of the year where the sample was collected, rows panels corresponds to the study areas, and column panels represents each Drug. Colors were assigned based on the possible phenotype, blue indicates sensitive, red indicates resistance, and gloden represent haplotypes carrying mutations respect to the reference strain but that haven’t been associated with resistance. 

drug_resistant_haplotypes_plot$haplotypes_freq_lineplot
**Figure 4:** Frequency of haplotypes of genes that carry mutations associated with resistance to Chloroquine, Lumefantrine...(panels). y-axis shows the frequency in each population, x-axis shows the quarter of the year where the sample was collected, rows panels corresponds to the study areas, and column panels represents each Drug. Colors were assigned based on the possible phenotype, blue indicates sensitive, red indicates resistance (and the intensity the number of mutations), and orange represent haplotypes carrying mutations respect to the reference strain but that haven't been associated with resistance.

Figure 4: Frequency of haplotypes of genes that carry mutations associated with resistance to Chloroquine, Lumefantrine…(panels). y-axis shows the frequency in each population, x-axis shows the quarter of the year where the sample was collected, rows panels corresponds to the study areas, and column panels represents each Drug. Colors were assigned based on the possible phenotype, blue indicates sensitive, red indicates resistance (and the intensity the number of mutations), and orange represent haplotypes carrying mutations respect to the reference strain but that haven’t been associated with resistance. 

drug_resistant_haplotypes_plot$haplotype_freq_barplot
**Figure 5:** Frequency of haplotypes of genes that carry mutations associated with resistance to Chloroquine, Lumefantrine...(panels). y-axis shows the frequency in each population, x-axis shows the quarter of the year where the sample was collected, rows panels corresponds to the study areas, and column panels represents each Drug. Colors were assigned based on the possible phenotype, blue indicates sensitive, red indicates resistance (and the intensity the number of mutations), and orange represent haplotypes carrying mutations respect to the reference strain but that haven't been associated with resistance.

Figure 5: Frequency of haplotypes of genes that carry mutations associated with resistance to Chloroquine, Lumefantrine…(panels). y-axis shows the frequency in each population, x-axis shows the quarter of the year where the sample was collected, rows panels corresponds to the study areas, and column panels represents each Drug. Colors were assigned based on the possible phenotype, blue indicates sensitive, red indicates resistance (and the intensity the number of mutations), and orange represent haplotypes carrying mutations respect to the reference strain but that haven’t been associated with resistance. 

drug_resistant_haplotypes_plot$genotype_phenotype_table %>%
  DT::datatable(extensions = 'Buttons',
                options = list(dom = 'Blfrtip',
                  buttons = c('csv', 'excel')))
drug_resistant_haplotypes_plot$drug_phenotype_table %>%
  DT::datatable(extensions = 'Buttons',
                options = list(dom = 'Blfrtip',
                  buttons = c('csv', 'excel')))
drug_resistant_haplotypes_plot$aa_mutations %>%
  DT::datatable(extensions = 'Buttons',
                options = list(dom = 'Blfrtip',
                  buttons = c('csv', 'excel')))
drug_resistant_haplotypes_plot$dna_mutations %>%
  DT::datatable(extensions = 'Buttons',
                options = list(
                  buttons = c('csv', 'excel')))